Variant report

Variant	rs12049572
Chromosome Location	chr1:113140583-113140584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113138487..113142157-chr1:113142308..113146273,3	K562	blood:
2	chr1:113139489..113141863-chr1:113160606..113162292,2	K562	blood:
3	chr1:113139567..113142157-chr1:113143590..113146632,3	K562	blood:

Variant related genes	Relation type
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10857961	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10857964	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10857967	0.86[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1106287	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11102496	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102498	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102513	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102514	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102522	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs12029985	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12030612	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12030641	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12040988	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12045227	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12117479	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12120956	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12122980	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12126684	0.83[AMR][1000 genomes]
rs12126971	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12130243	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12137269	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12140506	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406530	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12724928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12756815	0.94[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17030613	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17030651	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2009056	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2064711	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273368	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2306937	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2306940	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2887882	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34107138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34199214	0.82[EUR][1000 genomes]
rs34569066	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35023236	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35147679	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3737136	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3748656	0.89[CEU][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs3790606	0.86[CHB][hapmap]
rs3795819	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs55652172	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56135413	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60900293	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61818802	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6679	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7522283	0.82[JPT][hapmap]
rs9308256	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12049572	SYT6	cis	parietal	SCAN
rs12049572	AMPD1	cis	cerebellum	SCAN
rs12049572	DENND2C	cis	parietal	SCAN
rs12049572	ST7L	cis	multi-tissue	Pritchard
rs12049572	ST7L	cis	lymphoblastoid	seeQTL
rs12049572	WNT2B	cis	parietal	SCAN
rs12049572	GSTM1	cis	parietal	SCAN
rs12049572	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs12049572	SLC16A4	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
2	chr1:113109000-113160000	Weak transcription	Gastric	stomach
3	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
5	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
6	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
7	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:113121000-113148400	Weak transcription	Stomach Mucosa	stomach
10	chr1:113124600-113148400	Weak transcription	NHLF	lung
11	chr1:113125000-113142000	Weak transcription	Hela-S3	cervix
12	chr1:113126800-113143400	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:113128000-113148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:113129000-113147200	Strong transcription	HSMM	muscle
15	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:113130200-113141000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
18	chr1:113131600-113147200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:113132600-113148400	Weak transcription	Lung	lung
20	chr1:113132600-113148400	Weak transcription	Pancreas	Pancrea
21	chr1:113132600-113148400	Weak transcription	Thymus	Thymus
22	chr1:113132600-113152400	Weak transcription	Psoas Muscle	Psoas
23	chr1:113132600-113154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:113132800-113143400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:113132800-113144200	Weak transcription	Right Ventricle	heart
27	chr1:113132800-113145400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:113133000-113142000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:113133000-113142600	Weak transcription	Aorta	Aorta
30	chr1:113133000-113143400	Weak transcription	HepG2	liver
31	chr1:113133000-113143800	Weak transcription	Ovary	ovary
32	chr1:113133000-113148400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:113133000-113148400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:113133000-113148600	Weak transcription	HSMMtube	muscle
35	chr1:113133000-113152000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:113133000-113152400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
38	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:113133200-113141800	Weak transcription	K562	blood
40	chr1:113133200-113142600	Weak transcription	Brain Germinal Matrix	brain
41	chr1:113133200-113143600	Weak transcription	Brain Angular Gyrus	brain
42	chr1:113133200-113144200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:113133200-113146800	Weak transcription	Fetal Thymus	thymus
44	chr1:113133200-113148400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:113133200-113148400	Weak transcription	GM12878-XiMat	blood
46	chr1:113133200-113148600	Weak transcription	A549	lung
47	chr1:113133200-113149800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:113133200-113150800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:113133200-113159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:113133200-113159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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